Doctrine: Why can't I free memory when accessing entities through an association?

Cascade

EntityManager::detach should indeed remove all references Doctrine has to the enities. But it does not do the same for associated entities automatically.

You need to cascade this action by adding detach the cascade option of the association:

/**
 * @ORM\OneToMany(
 *   targetEntity="AppBundle\Entity\ApplicationFile",
 *   mappedBy="application",
 *   cascade={"remove", "detach"},
 *   orphanRemoval=true
 * )
 */
private $files;

Now $em->detach($app) should be enough to remove references to the Application entity as well as its associated ApplicationFile entities.

Find vs Collection

I highly doubt that loading the ApplicationFile entities through the association, in stead of using the repository to findBy() them, is the source of your issue.

Sure that when loaded through the association, the Collection will have a reference to those child-entities. But when the parent entity is dereferenced, the entire tree will be garbage collected, unless there are other references to those child entities.

I suspect the code you show is pseudo/example code, not the actual code in production. Please examine that code thoroughly to find those other references.

Clear

Sometimes it worth clearing the entire EntityManager and merging a few entities back in. You could try $em->clear() or $em->clear('AppBundle\Entity\ApplicationFile').

Clear has no effect

You're saying that clearing the EntityManager has no effect. This means the references you're searching for are not within the EntityManager (of UnitOfWork), because you've just cleared that.

Doctrine but not Doctrine

Are you using any event-listeners or -subscribers? Any filters? Any custom mapping types? Multiple EntityManagers? Anything else that could be integrated into Doctrine or its life-cycle, but is not necessarily part of Doctrine itself?

Especially event-listeners/subscribers are often overlooked when searching for the source of issues. So I'd suggest you start to look there.